RetrogeneDB ID: retro_fcat_809

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: B3:71405..71933(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: CCND2
• Ensembl ID: ENSFCAG00000000138
• Aliases: None
• Description: cyclin D2 [Source:HGNC Symbol;Acc:1583]

Sequence

>retro_fcat_809
GAGACCACCCCTCTAACAGCAGAGAAGTTGTGCATTTACACCAACAACTCCATCAAACCTCAGGAGCTGCTGGAGTGGGA
GCTGGTGGTGTTGGGGAAGTTGAAGTGGAACCTGGCGGCTATCACTCCTCACGACCTCATCTAGCACATCCTTCGCAAGC
TGCCCCAGCCCAGCAAGAAGTTGTCTTTGATCCGCAAGCATGCACAGACTTTCATTGCTCTGTGTGCTACCAACTTTAAG
CTCGCCATGTACCTGCCATCGATGATTGCAACTGGAAGTGTTGGAGTCGCCATCTATGGGCTCCACCAGGATGAGGACGT
GAGCTCACACACCAGTAATGCCCTGGTAGATCTGCTGGTCAAGATCACCAACACAGATGTGGACTGCCTCAAAGCCTTCC
AGGAGCAGATTGAGGTGGTACTGCTCAACGGCCTGCAGTATTTCTGTCAGGACCAGGGGGATGGGTCCAAGCCAGAGGAT
GAACTGGACCAGGCCAGCACCCCTACAGATGTGCGGGATATTGACCTG

Alignment

ORF - retro_fcat_809 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.07 %
• Parental protein coverage: 60.48 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ETIPLTAEKLCIYTDNSIKPQELLEWELVVLGKLKWNLAAVTPHDFIEHILRKLPQPSEKLSLIRKHAQT
          ET.PLTAEKLCIYT.NSIKPQELLEWELVVLGKLKWNLAA.TPHD.I.HILRKLPQPS.KLSLIRKHAQT
Retrocopy ETTPLTAEKLCIYTNNSIKPQELLEWELVVLGKLKWNLAAITPHDLI*HILRKLPQPSKKLSLIRKHAQT

Parental  FIALCATDFKFAMYPPSMIATGSVGAAICGLQQDEDVSSLTGDALVDLLAKITNTDVDCLKACQEQIEVV
          FIALCAT.FK.AMY.PSMIATGSVG.AI.GL.QDEDVSS.T..ALVDLL.KITNTDVDCLKA.QEQIEVV
Retrocopy FIALCATNFKLAMYLPSMIATGSVGVAIYGLHQDEDVSSHTSNALVDLLVKITNTDVDCLKAFQEQIEVV

Parental  LLNSLQQFRQDQGDGSKSEDELDQASTPTDVRDIDL
          LLN.LQ.F.QDQGDGSK.EDELDQASTPTDVRDIDL
Retrocopy LLNGLQYFCQDQGDGSKPEDELDQASTPTDVRDIDL

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP017611_brain	0.00 RPM	35.12 RPM
SRP017611_kidney	0.00 RPM	2.58 RPM
SRP017611_liver	0.10 RPM	1.52 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_809 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_809 was not experimentally validated.

Homology

Retrocopy orthology:

Felis catus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000001593	1 retrocopy	retro_cjac_3884,
Felis catus	ENSFCAG00000000138	1 retrocopy	retro_fcat_809 ,
Felis catus	ENSFCAG00000001572	1 retrocopy	retro_fcat_840,
Oryctolagus cuniculus	ENSOCUG00000015589	1 retrocopy	retro_ocun_1277,
Otolemur garnettii	ENSOGAG00000005208	1 retrocopy	retro_ogar_977,